############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 33 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2024-12-11 03:54:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-11 03:54:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:41] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Contains 1 files. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-11 03:54:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-12-11 03:54:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-11 03:54:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-11 03:54:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-11 03:54:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-11 03:54:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:41] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2024-12-11 03:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-11 03:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Contains 1 files. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-11 03:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-12-11 03:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-11 03:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-11 03:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-11 03:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-11 03:54:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-11 03:54:53] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 85.188 0.045 87.975 curated_ligrec_stats 28.813 1.473 107.897 omnipath-interactions 21.460 2.195 65.762 filter_extra_attrs 15.150 0.101 15.838 with_extra_attrs 14.481 0.283 19.874 pivot_annotations 12.994 0.943 37.992 static_table 11.079 0.469 21.217 translate_ids_multi 11.027 0.506 26.979 nichenet_gr_network_omnipath 10.689 0.473 22.848 go_annot_download 9.160 0.688 10.294 extra_attr_values 8.758 0.200 14.590 extra_attrs_to_cols 8.827 0.042 8.871 giant_component 7.602 0.356 14.772 omnipath_for_cosmos 7.428 0.411 20.271 print_interactions 7.596 0.222 15.703 nichenet_signaling_network_omnipath 7.160 0.423 12.981 pubmed_open 6.841 0.010 7.423 has_extra_attrs 5.994 0.118 6.227 filter_by_resource 5.689 0.112 12.439 filter_intercell 4.684 0.366 14.018 curated_ligand_receptor_interactions 4.404 0.598 17.840 signed_ptms 4.418 0.071 5.332 print_path_vs 3.229 0.044 6.368 enzsub_graph 1.816 0.043 5.090 uniprot_full_id_mapping_table 1.700 0.017 24.378 ensembl_id_mapping_table 1.062 0.054 11.199 translate_ids 0.973 0.032 18.467 all_uniprots 0.883 0.063 23.188 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.